Background: Integrated Treatment (IT) has proved effective in treating patients with Substance Use Disorders (SUD) co-occurring with severe Mental Disorders (MD), less is known about the effectiveness of IT for patients with SUD co-occurring with less severe MD.The aim of this study was to investigate the effectiveness of IT for patients with SUD co-occurring with anxiety and/or depression on the following parameters:1. The use of substances, as measured by the Alcohol Use Identification Test (AUDIT), the Drug Use Identification Test (DUDIT), and the Addiction Severity Index (EuropASI).2. The severity of psychiatric symptoms, as measured by the Symptom Check List 90 r (SCL 90R).3. The client’s motivation for changing his/her substance use behaviour, as measured by the Substance Abuse Treatment Scale (SATSr). Methods: This is a group randomized clinical trial comparing the effectiveness of IT to treatment as usual in Community Mental Health Centres (CMHCs). Five CMHCs were drawn to the Intervention Group (IG) and four CMHCs to the Control Group (CG). The allocation to treatment conditions was not blinded. New referrals were screened with the AUDIT and the DUDIT. Those who scored above the cut-off level of these instruments were assessed with the Structured Clinical Interview for DSM-IV 1 and 2. We included patients with anxiety and/or depression together with one or more SUDs. Results: We included 55 patients in the IG and 21 in the CG. A linear multilevel model was used. Both groups reduced their alcohol and substance use during the trial, while there was no change in psychiatric symptoms in either group. However, the IG had a greater increase in motivation for substance use treatment after 12 months than had the CG with an estimate of 1.76, p = 0.043, CI95% (0.08; 3.44) (adjusted analyses). There were no adverse events. Conclusions: Integrated treatment is effective in increasing the motivation for treatment amongst patients with anxiety and/or depression together with SUD in outpatient clinics. Trial registration: ClinicalTrials.gov: NCT00447733.